Autophagy is a catabolic mechanism responsible for the turn-over of long-lived proteins and organelles. It serves an essential role during development, starvation and infections. Furthermore, dysregulation of autophagy has been linked to diseases one of them being cancer. However, detection of autophagosomes in patient samples is limited by relatively poor antibodies against the few known autophagosomal markers. Thus, identification of new autophagosomal markers, and raising antibodies against these, will be of major importance.In this study we applied quantitative mass spectrometry analysis to identify autophagsome-associated proteins. We starved breast cancer cells expressing GFP-LC3 or treated them with rapamycin or concanamycin A, purified their autophagosomes by gradient centrifugation and analyzed the protein composition by mass spectrometry. We identified several hundred proteins in the purified autophagosomes. Interestingly, only a small subset of these was common for the starved cells and cells treated with rapamycin and concanamycin A. The known autophagosome-associated proteins, GABARAPL2 and p62/SQSTMN1, were among the common proteins. Notably, the majority of the autophagosome-associated proteins were specific to the insult applied. This suggests that an autophagosome selectively chooses the proteins to be degraded, instead of serving as a non-selective degradation mechanism. Importantly, we found 85 common autophagosome-associated proteins. We are currently testing by immune-staining if these could serve as new autophagosomal markers.